The Jane Does
Officer Beadie Russell deals with various agencies trying to decide who has to take responsibility for investigating the deaths of the thirteen girls in a cargo container. Coroner Randall Frazier establishes the cause of death as suffocation because of a crushed air pipe on the top of the container. The damage to the air supply is deemed accidental due to cargo moving. The case is handed back to Beadie because the deaths are considered accidental.
Detective Bunk Moreland and Officer Jimmy McNulty enjoy some crabs, a perk of McNulty's new assignment. McNulty insists the door stay shut, as he is avoiding Colonel Rawls. Bunk learns that McNulty spent three hours working out where a floating body was dumped in order to establish that it fell under Rawls' jurisdiction. Bunk chastises him for dumping the case on Detective Ray Cole, but McNulty dismisses Cole's troubles as collateral damage. McNulty leaves his shift on the boat early, leaving his partner Claude Diggins to tie the knots. He visits the container and discusses the case with Beadie Russell. He thinks there may be a link between the girls in the container and his floater, and Beadie tells him about an extra bedroll in the container. McNulty checks the crushed air pipe and notes that it appears to have been crushed deliberately. Beadie and McNulty meet with the coroner, who agrees that this is grounds to consider the girls murdered.
Rawls meets with Ronnie, the commander of the port police, and resists an attempt to hand off the thirteen murders. Landsman's homicide squad, now including Lester Freamon, watches Rawls with palpable anticipation as he leaves the meeting; he announces his success with a raised fist as he returns to his office. Meanwhile, McNulty convinces the coroner to estimate time of death based on the amount of air in the container to see if it matches when the other girl was dumped in the water. Rawls later meets with the commanders of all the other jurisdictions involved with the bodies. Despite his protestations, they insist that the murders occurred in his jurisdiction. The cases are assigned to Landsman's squad, who can only look on crestfallen as they are written up on the board.
Freamon, Bunk, and McNulty drink themselves into a state at their regular bar. The homicide detectives have bought fourteen shots for McNulty to mark the cases he brought to them. They have several laughs at Burrell, Rawls, Landsman, and Cole's expense. When they return to the detail, Landsman tells them Cole is working their cases while they are assigned the Jane Does from the port. Landsman tells them he needs the cases solved and they are his best detectives, so they get the case. Cole delights in handing over his work so far. Freamon and Bunk later travel to the Port Authority police department and meet with Beadie. When she asks if they know McNulty, Bunk's reply is a deadpan "He's dead to us." They begin to interrogate the crew of the ship.
Rhonda Pearlman and McNulty continue their casual relationship despite his drunken stupor. She questions their relationship's direction and tells him not to come to her house again. He admits he still hopes to reconcile with his wife for his children's sake, which prompts her to walk away from him.
Lieutenant Cedric Daniels walks with his wife Marla after a restaurant meal and she apologizes for bringing up his career. Lt. Daniels tells Marla that he will hand in his walking papers.
Stevedore union leader Frank Sobotka has an angry meeting with his smuggling contact Spiros "Vondas" Vondopoulos in The Greek's cafe regarding the dead girls on the docks. His nephew Nick Sobotka tries to talk him down before the meeting, but Frank will not be swayed. Frank is concerned that the deaths were deliberate and that he could have prevented them if he had known there were girls in the container. Vondas reassures him that the deaths were accidental and explains that their driver Sergei "Serge" Malatov was waiting for a contact to come off the ship and signal him that it was safe to take the container. Frank asks to be informed next time human cargo moves through the docks despite Vondas's assurance that he does not want to know. After the meeting, Vondas speaks to another man in the cafe, who happens to be The Greek himself.
Back at the union house, Thomas "Horseface" Pakusa complains to Frank that the port police are hassling him over some missing cases of vodka. He admits taking four cases, but denies breaking the seal; Frank is unconcerned. Ott then comes in complaining that the police are ticketing their cars. Frank approaches an officer who turns out to be Sergeant Ellis Carver, back in uniform. Frank sees they are being ticketed on frivolous charges ("License plate not entirely visible") and complains accordingly. Carver reveals that the ticketing is not his idea, he has been ordered to ticket the dock workers' vehicles twice a day from his shift lieutenant who passed the orders down from their district Major Stan Valchek, whom Frank knows and refers to as a "gaping asshole." Carver then states that he personally disagrees with ticketing their cars but is doing so because the chain of command in his district (in particular Major Valchek) see matters differently. As Frank states the union is going to city hall to fight the ticketing, Carver does not disagree with their decision and pleads for the union to only go after Valchek as he is the one who ordered the ticketing.
The next day, Valchek comes to the union hall where he angrily accuses Frank of illegally funding the stained glass window that is present in their church. Frank dismisses Valchek's threats and reminds him that they came from the same neighborhood and people still talk about Valchek's shortcomings. After his disappointing confrontation, Valchek visits a property developer friend, Andy Krawczyk, to discuss trying to reclaim his donation from the church. He learns that Frank Sobotka's union have been making political contributions, hired a lobbyist, and generally show a lot of cash for a failing industrial organization. Krawcyzk then comments about Burrell's nomination for commissioner in which Valchek claims "I've seen worse." Valchek then meets with Deputy Commissioner Burrell and talks about his nomination for police commissioner. Valchek has noticed that Burrell has a political nomination from the mayor and almost every city council district except for those in the first district (Valchek's base), a district populated by white ethnics who have a history for not supporting the city's African American political and police figures such as Burrell. Valchek then suggests he can use his political influence to get the first district to vote Burrell in and realizing Valchek's nature, Burrell then asks what Valchek wants in return. Feigning surprise, Valchek then request a detail for the investigation of Frank Sobotka's union. Valchek claims that their union is probably involved in thieving or smuggling at the port and then states his personal dislike for Sobotka. Burrell agrees to have Rawls organize a squad of six men for six weeks.
Nick, Ziggy Sobotka and the other Stevedores drink at Delores's bar at breakfast time. Ziggy discusses a connection named "White Mike" who can supply them with drugs. He wants Nick to partner with him in buying the package and selling it off, but Nick refuses his offer. Ott announces that a ship is in and gives Nick a ride. The dock workers are stopped on the way by patrol officers led by Carver who have established a D.W.I. checkpoint courtesy of Valchek. As they step out of the car, Ott claims that a breathalyzer at 8 in the morning is unheard of. Ziggy meets White Mike alone and asks him to give him the package with payment to follow. Ziggy has messed up his last two attempts, so Mike refuses to trust him again. After being released from Central Booking on D.U.I. charges, the Stevedores, particularly Ott, complain to Frank about the police activity. Frank admits to his rivalry with Valchek. They insist he deal with the problem and Frank tells Nick that if Valchek wants a war he will have one. Horseface later infiltrates Valchek's district's parking lot and steals a surveillance van filled with equipment. He drives it to the docks and La La, Frank, and Nick help him load it into a container.
Brianna Barksdale visits her brother Avon in prison and pleads with him to look out for her son D'Angelo, as he took a 20 year sentence for their family. They also discuss the loss of their New York connection, Roberto. Brianna tells him their money has been returned and that Stringer Bell had to deal with the Dominicans' lawyer because they fear it is unsafe to deal with the Barksdale organization with Avon imprisoned. Avon recommends a contact named Vargas, who owns a wheel rim shop in Atlanta. Brianna also tells Avon that D'Angelo's girlfriend Donette has been out of touch, and Avon has also noticed that she has not visited D'Angelo.
Wee-Bey Brice's cell is later searched by a guard named Tilghman who is physically aggressive toward him, takes his magazines, upends his fish tank (filled with plastic fish), and tears down his posters. Wee-Bey complains to Avon that the guard, Tilghman, is deliberately targeting him because he is the cousin of one of the victims he was convicted of murdering. Avon agrees to meet with Tilghman, but is almost instantly rebuffed when he approaches him.
Stringer later visits Avon at the prison and tells him that the Atlanta contact has been put into play. Avon tells Stringer he needs to help him deal with Tilghman and also find Donette and ensure she visits D'Angelo regularly. Stringer checks with Avon about D'Angelo's loyalty and Avon insists that D can be trusted to handle his burden, as he is family.
Avon finds D'Angelo is sniffing a powdery substance in his cell with another inmate. He asks D'Angelo how he is getting on and tells him they need to talk.
Valchek assembles and briefs his new detail in their port side offices. He tells them that Lieutenant Grayson will command the detail and that his son-in-law Prez is a prodigy of his and lead investigator. Valchek does not realize that Burrell has pulled the same stunt as he had with Lieutenant Daniels in Season 1; Burrell has sent Valchek the most incompetent officers in the department who are dead weight in their respective units. This is proven by the alcoholic Detective Polk whose only concern is who signs off on their overtime.
Loose ends for the Greek
Sergei "Serge" Malatov travels out of town with a taciturn associate and they infiltrate another port in Philadelphia using fake Coast Guard IDs. He orders the ship held in port, which prompts one of the crew to come ashore. They chase a crewman down with their car, beat him up, and bundle him into the backseat.
Sergei and his associate violently interrogate the now naked crewman, Sam, and ask him why he fled the Atlantic Light. The Greek and Spiros "Vondas" Vondopoulos arrive and The Greek initially appears to have a more generous disposition. He notices Sam's tattoos and identifies him as Turkish. Sam admits that he let his crew have sex with the girls in exchange for money after he let them out of the container. One of his men killed the girl who was dumped overboard and the other girls saw, so he had them all killed. Once Sam's tale is finished, Spiros slowly cuts his throat. The Greek orders Sergei to ensure that there are no finger prints or face on the corpse.